package annotate.encode;

import java.io.BufferedWriter;
import java.io.FileWriter;

public class Commons {
	
	
	public static Integer ZERO = new Integer(0); 
	public static Long LONG_ZERO = new Long(0); 
	
	public static final String HYPHEN = "HYPHEN";
	public static final String TEST_LINEAR_SEARCH_VERSUS_INTERVAL_TREE_SEARCH ="C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\testlinearsearchversusintervaltreesearch\\input_output\\Compare.txt";
	
	public static int NUMBER_OF_CHROMOSOMES_HG19 = 24;
	
//	Calculations
	public static final String HG19_CHROMOSOME_SIZES_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\calculations\\input_output\\hg19.chrom.sizes.txt";
	public static final String NUMBER_OF_OCCURRENCES_OF_EACH_DNASE_CELL_LINE_WHOLE_GENOME_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\calculations\\input_output\\number_of_occurrences_of_dnaseCellLine_on_nonoverlapping_base_pairs_whole_genome.txt";
	public static final String NUMBER_OF_OCCURRENCES_OF_EACH_DNASE_CELL_LINE_SEARCH_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\dnase_results.txt";
	
	public static final String NUMBER_OF_OCCURRENCES_OF_EACH_TFBS_WHOLE_GENOME_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\calculations\\input_output\\number_of_occurrences_of_tfbs_on_nonoverlapping_base_pairs_whole_genome.txt";
	
	public static final String NUMBER_OF_OCCURRENCES_OF_EACH_HISTONE_WHOLE_GENOME_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\calculations\\input_output\\number_of_occurrences_of_histone_on_nonoverlapping_base_pairs_whole_genome.txt";
	
//	Write all possible names
	public static final String DNASE = "DNASE";
	public static final String TFBS = "TFBS";
	public static final String HISTONE = "HISTONE";
	public static final String UCSC_GENE = "UCSC_GENE";
	public static final String NCBI_GENE_ID = "NCBI_GENE_ID";
	public static final String NCBI_RNA_NUCLEOTIDE_ACCESSION_VERSION = "NCBI_RNA_NUCLEOTIDE_ACCESSION_VERSION";
	public static final String UCSC_GENE_ALTERNATE_NAME = "UCSC_GENE_ALTERNATE_NAME";
	public static final String KEGG_PATHWAY = "KEGG_PATHWAY";
	
	
	public static final String ANNOTATE_INTERVALS_DNASE_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\dnase_results.txt";
	public static final String ANNOTATE_INTERVALS_TFBS_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\tfbs_results.txt";
	public static final String ANNOTATE_INTERVALS_HISTONE_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\histone_results.txt";
	public static final String ANNOTATE_INTERVALS_NCBI_GENE_ID_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\ncbi_gene_id_results.txt";
	public static final String ANNOTATE_INTERVALS_NCBI_RNA_NUCLEOTIDE_ACCESSION_VERSION_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\ncbi_rna_results.txt";
	public static final String ANNOTATE_INTERVALS_UCSC_GENE_ALTERNATE_NAME_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\ucsc_gene_alternate_name_results.txt";
	public static final String ANNOTATE_INTERVALS_KEGG_PATHWAY_RESULTS_OUTPUT_FILE =  "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\results\\kegg_pathway_results.txt";
	
// 	All possible names		
	public static final String WRITE_ALL_POSSIBLE_DNASE_CELL_NAMES_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_dnase_cell_lines_names.txt";
	public static final String WRITE_ALL_POSSIBLE_TFBS_NAMES_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_tfbs_names.txt";
	public static final String WRITE_ALL_POSSIBLE_HISTONE_NAMES_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_histone_names.txt";
	public static final String WRITE_ALL_POSSIBLE_GENE_IDS_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_gene_ids.txt";	
	public static final String WRITE_ALL_POSSIBLE_RNA_NUCLEUOTIDE_ACCESSION_VERSIONS_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_rna_nucleotide_accession_versions.txt";	
	public static final String WRITE_ALL_POSSIBLE_ALTERNATE_GENE_NAMES_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_alternate_gene_names.txt";	
	public static final String WRITE_ALL_POSSIBLE_KEGG_PATHWAY_NAMES_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\all_possible_names\\all_possible_kegg_pathway_names.txt";
	
//	Kegg Pathway to Ncbi Ref Seq Gene Ids
	public static final String KEGG_PATHWAY_2_NCBI_GENE_IDS_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\keggpathway\\ncbigenes\\input_output\\pathway_hsa.list";
	public static final String ALL_POSSIBLE_KEGG_PATHWAY_NAMES_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\keggpathway\\ncbigenes\\input_output\\all_possible_kegg_pathway_names.txt";
	public static final String KEGG_PATHWAY_2_NCBI_GENE_IDS_OUTPUT_FILE_PATH = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\keggpathway\\ncbigenes\\input_output\\";
	
	
//	Annotate intervals using interval tree
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\SearchInputforTCGATestData.txt";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_REGULOMEDB_EXAMPLE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\SearchRegulomeDBInputExampleData.txt";
	public static final String ANNOTATE_INTERVALS_WITH_DNASE_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\dnase_cell_line_names.txt";
	public static final String ANNOTATE_INTERVALS_WITH_TFBS_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\tfbs_names.txt";
	public static final String ANNOTATE_INTERVALS_WITH_HISTONE_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\histone_names.txt";
	public static final String ANNOTATE_INTERVALS_WITH_NCBI_GENE_ID_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\gene_ids.txt";
	public static final String ANNOTATE_INTERVALS_WITH_NCBI_RNA_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\rna_nucleotide_accession_versions.txt";
	public static final String ANNOTATE_INTERVALS_WITH_UCSC_ALTERNATE_GENE_NAME_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\alternate_gene_names.txt";	
	public static final String ANNOTATE_INTERVALS_WITH_KEGG_PATHWAY_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\kegg_pathway_names.txt";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\Annotate_SearchOutputforTCGATestData.txt";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\dnase\\";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\tfbs\\";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\histone\\";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_NCBI_GENE_ID = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\ncbiGeneId\\";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_NCBI_RNA = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\ncbiRNA\\";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_UCSC_GENE_ALTERNATE_NAME = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\ucscGeneAlternateName\\";
	public static final String ANNOTATE_INTERVALS_USING_INTERVAL_TREE_OUTPUT_FILE_PATH_FOR_KEGG_PATHWAY = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\intervals\\parametric\\input_output\\keggPathway\\";
		
//	Search using Linear search
	public static final String SEARCH_USING_LINEAR_SEARCH_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\SearchInputforTCGATestData.txt";
	public static final String SEARCH_USING_LINEAR_SEARCH_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\Linear_Search_SearchOutputforTCGATestData.txt";	
	
// 	Searching using IntervalTree 	
	public static final String SEARCH_USING_INTERVAL_TREE_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\SearchInputforTCGATestData.txt";
	public static final String SEARCH_USING_INTERVAL_TREE_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\Interval_Tree_SearchOutputforTCGATestData.txt";
	
	
	public static final String SEARCH_CHR1_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr1_input_file.txt";
	public static final String SEARCH_CHR2_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr2_input_file.txt";
	public static final String SEARCH_CHR3_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr3_input_file.txt";
	public static final String SEARCH_CHR4_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr4_input_file.txt";
	public static final String SEARCH_CHR5_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr5_input_file.txt";
	public static final String SEARCH_CHR6_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr6_input_file.txt";
	public static final String SEARCH_CHR7_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr7_input_file.txt";
	public static final String SEARCH_CHR8_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr8_input_file.txt";
	public static final String SEARCH_CHR9_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr9_input_file.txt";
	public static final String SEARCH_CHR10_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr10_input_file.txt";
	public static final String SEARCH_CHR11_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr11_input_file.txt";
	public static final String SEARCH_CHR12_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr12_input_file.txt";
	public static final String SEARCH_CHR13_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr13_input_file.txt";
	public static final String SEARCH_CHR14_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr14_input_file.txt";
	public static final String SEARCH_CHR15_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr15_input_file.txt";
	public static final String SEARCH_CHR16_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr16_input_file.txt";
	public static final String SEARCH_CHR17_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr17_input_file.txt";
	public static final String SEARCH_CHR18_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr18_input_file.txt";
	public static final String SEARCH_CHR19_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr19_input_file.txt";
	public static final String SEARCH_CHR20_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr20_input_file.txt";
	public static final String SEARCH_CHR21_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr21_input_file.txt";
	public static final String SEARCH_CHR22_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chr22_input_file.txt";
	public static final String SEARCH_CHRX_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chrX_input_file.txt";
	public static final String SEARCH_CHRY_INPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\search_chrY_input_file.txt";
	
	
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR1_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr1_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR2_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr2_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR3_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr3_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR4_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr4_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR5_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr5_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR6_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr6_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR7_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr7_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR8_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr8_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR9_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr9_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR10_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr10_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR11_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr11_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR12_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr12_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR13_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr13_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR14_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr14_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR15_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr15_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR16_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr16_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR17_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr17_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR18_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr18_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR19_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr19_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR20_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr20_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR21_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr21_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHR22_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chr22_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHRX_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chrX_ucsc_refseq_genes_interval_tree.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODEUCSCGENOME_SORTED_CHRY_UCSC_REFSEQ_GENES_INTERVAL_TREE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encodeucscgenome\\input_output\\sorted_chrY_ucsc_refseq_genes_interval_tree.txt";
			
	//Downloaded from ncbi, gene2refseq.txt data
	public static final String NCBI_GENE_TO_REF_SEQ = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\ncbi\\input_output\\gene2refseq.txt";	
	public static final String NCBI_HUMAN_GENE_TO_REF_SEQ = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\ncbi\\input_output\\human_gene2refseq.txt";
	public static final String NCBI_HUMAN_REF_SEQ_TO_GENE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\ncbi\\input_output\\human_refseq2gene.txt";
	public static final String NCBI_HUMAN_REF_SEQ_TO_GENE_2 = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\ncbi\\input_output\\human_refseq2gene2.txt";
		
//	These files have been downloaded from ftp.ebi.ac.uk
//	They have been unzipped.
//	These files are yet unprocessed. 
//	They will be processed and will be accumated in corresponding chromosome base files first in unsorted manner then in sorted manner.
	public static final String TRANSCRIPTION_FACTOR_FILES_DIRECTORY = "C:\\eclipse_ganymede\\workspace\\ftp_encode\\transcription_factors";
	public static final String HISTONE_MARK_FILES_DIRECTORY = "C:\\eclipse_ganymede\\workspace\\ftp_encode\\histone_macs";
	public static final String DNASE_JUL2010_FILES_DIRECTORY = "C:\\eclipse_ganymede\\workspace\\ftp_encode\\dnase_jul2010";
	public static final String DNASE_FILES_DIRECTORY = "C:\\eclipse_ganymede\\workspace\\ftp_encode\\dnase";
	
	
	public static final String SEARCH_INPUT_FILE_WITH_HUGO_SYMBOL_ENTREZ_GENE_ID_COLUMN = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\testtcgadata\\input_output\\SearchInputWithHugoSymbolEntrezGeneIdColumns.txt";
	public static final String SEARCH_INPUT_FILE_WITH_NON_BLANK_SNP_IDS= "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\testtcgadata\\input_output\\SearchInputWithNonBlankSNPIDs.txt";
	public static final String SEARCH_INPUT_FILE_FOR_TCGA_TEST_DATA = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\testtcgadata\\input_output\\SearchInputforTCGATestData.txt";
	public static final String SEARCH_INPUT_FILE_FOR_TCGA_DATA_WITH_NON_BLANK_SNP_ROWS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\testtcgadata\\input_output\\SearchInputTCGADataWithNonBlankSNPRows.txt";
	public static final String SEARCH_OUTPUT_FILE_FOR_TCGA_TEST_DATA = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\testtcgadata\\input_output\\SearchOutputforTCGATestData.txt";
	
	
	public static final String SEARCH_OUTPUT_FILE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\SearchOutput.txt";
	
	
	public static final String HG19_UCSC_REF_SEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\hg19_refseq_genes.txt"; 
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSC_HG19_REFSEQ_GENES_INTERVALS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\hg19_refseq_genes_intervals.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSC_ANALYZE_HG19_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\analyze_hg19_refseq_genes.txt";
	
	public static final String CHROMOSOME1 = "chr1";
	public static final String CHROMOSOME2 = "chr2";
	public static final String CHROMOSOME3 = "chr3";
	public static final String CHROMOSOME4 = "chr4";
	public static final String CHROMOSOME5 = "chr5";
	public static final String CHROMOSOME6 = "chr6";
	public static final String CHROMOSOME7 = "chr7";
	public static final String CHROMOSOME8 = "chr8";
	public static final String CHROMOSOME9 = "chr9";
	public static final String CHROMOSOME10 = "chr10";
	public static final String CHROMOSOME11 = "chr11";
	public static final String CHROMOSOME12 = "chr12";
	public static final String CHROMOSOME13 = "chr13";
	public static final String CHROMOSOME14 = "chr14";
	public static final String CHROMOSOME15 = "chr15";
	public static final String CHROMOSOME16 = "chr16";
	public static final String CHROMOSOME17 = "chr17";
	public static final String CHROMOSOME18 = "chr18";
	public static final String CHROMOSOME19 = "chr19";
	public static final String CHROMOSOME20 = "chr20";
	public static final String CHROMOSOME21 = "chr21";
	public static final String CHROMOSOME22 = "chr22";
	public static final String CHROMOSOMEX = "chrX";
	public static final String CHROMOSOMEY = "chrY";
	
	
	//Unsorted Chromosome Base RefSeq Gene Files
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR1_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr1_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR2_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr2_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR3_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr3_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR4_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr4_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR5_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr5_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR6_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr6_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR7_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr7_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR8_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr8_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR9_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr9_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR10_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_ch10_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR11_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr11_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR12_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr12_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR13_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr13_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR14_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr14_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR15_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr15_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR16_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr16_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR17_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr17_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR18_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr18_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR19_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr19_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR20_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr20_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR21_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr21_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHR22_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chr22_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHRX_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chrX_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_UNSORTED_CHRY_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\unsorted_chrY_refseq_genes.txt";
	
	//Sorted Chromosome Base RefSeq Gene Files
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR1_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr1_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR2_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr2_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR3_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr3_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR4_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr4_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR5_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr5_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR6_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr6_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR7_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr7_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR8_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr8_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR9_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr9_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR10_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr10_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR11_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr11_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR12_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr12_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR13_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr13_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR14_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr14_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR15_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr15_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR16_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr16_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR17_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr17_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR18_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr18_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR19_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr19_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR20_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr20_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR21_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr21_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHR22_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chr22_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHRX_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chrX_refseq_genes.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_UCSCGENOME_SORTED_CHRY_REFSEQ_GENES = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\ucscgenome\\input_output\\sorted_chrY_refseq_genes.txt";
	
	
	// Unsorted Chromosome Base DNASE File names
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR1_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr1_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR2_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr2_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR3_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr3_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR4_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr4_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR5_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr5_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR6_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr6_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR7_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr7_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR8_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr8_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR9_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr9_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR10_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr10_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR11_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr11_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR12_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr12_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR13_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr13_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR14_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr14_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR15_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr15_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR16_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr16_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR17_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr17_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR18_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr18_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR19_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr19_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR20_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr20_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR21_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr21_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR22_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chr22_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHRX_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chrX_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHRY_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\unsorted_chrY_dnase.txt";	
	
	// Sorted Chromosome Base DNASE File names
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR1_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr1_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR2_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr2_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR3_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr3_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR4_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr4_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR5_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr5_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR6_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr6_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR7_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr7_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR8_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr8_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR9_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr9_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR10_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr10_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR11_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr11_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR12_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr12_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR13_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr13_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR14_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr14_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR15_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr15_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR16_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr16_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR17_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr17_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR18_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr18_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR19_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr19_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR20_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr20_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR21_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr21_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR22_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chr22_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHRX_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chrX_dnase.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHRY_DNASE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\dnase\\sorted_chrY_dnase.txt";

		
	
	// Unsorted Chromosome Base HISTONE File names
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR1_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr1_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR2_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr2_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR3_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr3_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR4_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr4_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR5_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr5_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR6_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr6_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR7_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr7_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR8_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr8_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR9_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr9_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR10_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr10_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR11_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr11_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR12_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr12_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR13_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr13_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR14_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr14_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR15_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr15_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR16_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr16_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR17_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr17_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR18_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr18_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR19_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr19_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR20_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr20_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR21_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr21_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR22_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chr22_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHRX_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chrX_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHRY_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\unsorted_chrY_histone.txt";	
	
	// Sorted Chromosome Base HISTONE File names
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR1_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr1_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR2_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr2_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR3_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr3_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR4_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr4_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR5_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr5_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR6_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr6_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR7_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr7_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR8_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr8_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR9_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr9_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR10_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr10_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR11_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr11_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR12_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr12_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR13_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr13_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR14_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr14_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR15_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr15_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR16_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr16_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR17_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr17_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR18_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr18_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR19_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr19_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR20_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr20_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR21_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr21_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR22_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chr22_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHRX_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chrX_histone.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHRY_HISTONE = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\histone\\sorted_chrY_histone.txt";

			
	// Unsorted Chromosome Base TFBS File names
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR1_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr1_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR2_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr2_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR3_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr3_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR4_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr4_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR5_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr5_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR6_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr6_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR7_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr7_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR8_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr8_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR9_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr9_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR10_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr10_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR11_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr11_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR12_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr12_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR13_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr13_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR14_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr14_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR15_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr15_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR16_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr16_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR17_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr17_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR18_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr18_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR19_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr19_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR20_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr20_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR21_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr21_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHR22_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chr22_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHRX_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chrX_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_UNSORTED_CHRY_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\unsorted_chrY_tfbs.txt";	
	
	// Sorted Chromosome Base TFBS File names
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR1_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr1_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR2_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr2_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR3_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr3_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR4_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr4_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR5_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr5_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR6_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr6_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR7_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr7_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR8_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr8_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR9_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr9_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR10_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr10_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR11_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr11_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR12_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr12_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR13_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr13_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR14_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr14_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR15_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr15_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR16_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr16_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR17_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr17_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR18_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr18_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR19_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr19_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR20_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr20_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR21_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr21_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHR22_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chr22_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHRX_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chrX_tfbs.txt";
	public static final String C_ECLIPSE_GANYMEDE_WORKSPACE_DOKTORA_ANNOTATE_ENCODE_SORTED_CHRY_TFBS = "C:\\eclipse_ganymede\\workspace\\Doktora1\\src\\annotate\\encode\\input_output\\tfbs\\sorted_chrY_tbs.txt";
		
//	Common FileWriters for Tfbs, Histone and Dnase Files
	FileWriter chr1FileWriter; 
	FileWriter chr2FileWriter; 
	FileWriter chr3FileWriter; 
	FileWriter chr4FileWriter; 
	FileWriter chr5FileWriter; 
	FileWriter chr6FileWriter; 
	FileWriter chr7FileWriter; 
	FileWriter chr8FileWriter; 
	FileWriter chr9FileWriter; 
	FileWriter chr10FileWriter; 
	FileWriter chr11FileWriter; 
	FileWriter chr12FileWriter; 
	FileWriter chr13FileWriter; 
	FileWriter chr14FileWriter; 
	FileWriter chr15FileWriter; 
	FileWriter chr16FileWriter; 
	FileWriter chr17FileWriter; 
	FileWriter chr18FileWriter; 
	FileWriter chr19FileWriter; 
	FileWriter chr20FileWriter; 
	FileWriter chr21FileWriter; 
	FileWriter chr22FileWriter; 
	FileWriter chrXFileWriter; 
	FileWriter chrYFileWriter; 
	
//	Common BuffredWriters for Tfbs, Histone and Dnase Files
	BufferedWriter chr1BufferedWriter;
	BufferedWriter chr2BufferedWriter;
	BufferedWriter chr3BufferedWriter;
	BufferedWriter chr4BufferedWriter;
	BufferedWriter chr5BufferedWriter;
	BufferedWriter chr6BufferedWriter;
	BufferedWriter chr7BufferedWriter;
	BufferedWriter chr8BufferedWriter;
	BufferedWriter chr9BufferedWriter;
	BufferedWriter chr10BufferedWriter;
	BufferedWriter chr11BufferedWriter;
	BufferedWriter chr12BufferedWriter;
	BufferedWriter chr13BufferedWriter;
	BufferedWriter chr14BufferedWriter;
	BufferedWriter chr15BufferedWriter;
	BufferedWriter chr16BufferedWriter;
	BufferedWriter chr17BufferedWriter;
	BufferedWriter chr18BufferedWriter;
	BufferedWriter chr19BufferedWriter;
	BufferedWriter chr20BufferedWriter;
	BufferedWriter chr21BufferedWriter;
	BufferedWriter chr22BufferedWriter;
	BufferedWriter chrXBufferedWriter;
	BufferedWriter chrYBufferedWriter;

	// Number of tfbs in each chromosome	
	int numberofTfbsinChr1 = 0;
	int numberofTfbsinChr2 = 0;
	int numberofTfbsinChr3 = 0;
	int numberofTfbsinChr4 = 0;
	int numberofTfbsinChr5 = 0;
	int numberofTfbsinChr6 = 0;
	int numberofTfbsinChr7 = 0;
	int numberofTfbsinChr8 = 0;
	int numberofTfbsinChr9 = 0;
	int numberofTfbsinChr10 = 0;
	int numberofTfbsinChr11 = 0;
	int numberofTfbsinChr12 = 0;
	int numberofTfbsinChr13 = 0;
	int numberofTfbsinChr14 = 0;
	int numberofTfbsinChr15 = 0;
	int numberofTfbsinChr16 = 0;
	int numberofTfbsinChr17 = 0;
	int numberofTfbsinChr18 = 0;
	int numberofTfbsinChr19 = 0;
	int numberofTfbsinChr20 = 0;
	int numberofTfbsinChr21 = 0;
	int numberofTfbsinChr22 = 0;
	int numberofTfbsinChrX = 0;
	int numberofTfbsinChrY = 0;

	// Number of histone in each chromosome	
	int numberofHistoneinChr1 = 0;
	int numberofHistoneinChr2 = 0;
	int numberofHistoneinChr3 = 0;
	int numberofHistoneinChr4 = 0;
	int numberofHistoneinChr5 = 0;
	int numberofHistoneinChr6 = 0;
	int numberofHistoneinChr7 = 0;
	int numberofHistoneinChr8 = 0;
	int numberofHistoneinChr9 = 0;
	int numberofHistoneinChr10 = 0;
	int numberofHistoneinChr11 = 0;
	int numberofHistoneinChr12 = 0;
	int numberofHistoneinChr13 = 0;
	int numberofHistoneinChr14 = 0;
	int numberofHistoneinChr15 = 0;
	int numberofHistoneinChr16 = 0;
	int numberofHistoneinChr17 = 0;
	int numberofHistoneinChr18 = 0;
	int numberofHistoneinChr19 = 0;
	int numberofHistoneinChr20 = 0;
	int numberofHistoneinChr21 = 0;
	int numberofHistoneinChr22 = 0;
	int numberofHistoneinChrX = 0;
	int numberofHistoneinChrY = 0;
	
	
	// Number of dnase in each chromosome	
	int numberofDnaseinChr1 = 0;
	int numberofDnaseinChr2 = 0;
	int numberofDnaseinChr3 = 0;
	int numberofDnaseinChr4 = 0;
	int numberofDnaseinChr5 = 0;
	int numberofDnaseinChr6 = 0;
	int numberofDnaseinChr7 = 0;
	int numberofDnaseinChr8 = 0;
	int numberofDnaseinChr9 = 0;
	int numberofDnaseinChr10 = 0;
	int numberofDnaseinChr11 = 0;
	int numberofDnaseinChr12 = 0;
	int numberofDnaseinChr13 = 0;
	int numberofDnaseinChr14 = 0;
	int numberofDnaseinChr15 = 0;
	int numberofDnaseinChr16 = 0;
	int numberofDnaseinChr17 = 0;
	int numberofDnaseinChr18 = 0;
	int numberofDnaseinChr19 = 0;
	int numberofDnaseinChr20 = 0;
	int numberofDnaseinChr21 = 0;
	int numberofDnaseinChr22 = 0;
	int numberofDnaseinChrX = 0;
	int numberofDnaseinChrY = 0;
	
	
	
	
	public int getNumberofDnaseinChr1() {
		return numberofDnaseinChr1;
	}

	public void setNumberofDnaseinChr1(int numberofDnaseinChr1) {
		this.numberofDnaseinChr1 = numberofDnaseinChr1;
	}

	public int getNumberofDnaseinChr2() {
		return numberofDnaseinChr2;
	}

	public void setNumberofDnaseinChr2(int numberofDnaseinChr2) {
		this.numberofDnaseinChr2 = numberofDnaseinChr2;
	}

	public int getNumberofDnaseinChr3() {
		return numberofDnaseinChr3;
	}

	public void setNumberofDnaseinChr3(int numberofDnaseinChr3) {
		this.numberofDnaseinChr3 = numberofDnaseinChr3;
	}

	public int getNumberofDnaseinChr4() {
		return numberofDnaseinChr4;
	}

	public void setNumberofDnaseinChr4(int numberofDnaseinChr4) {
		this.numberofDnaseinChr4 = numberofDnaseinChr4;
	}

	public int getNumberofDnaseinChr5() {
		return numberofDnaseinChr5;
	}

	public void setNumberofDnaseinChr5(int numberofDnaseinChr5) {
		this.numberofDnaseinChr5 = numberofDnaseinChr5;
	}

	public int getNumberofDnaseinChr6() {
		return numberofDnaseinChr6;
	}

	public void setNumberofDnaseinChr6(int numberofDnaseinChr6) {
		this.numberofDnaseinChr6 = numberofDnaseinChr6;
	}

	public int getNumberofDnaseinChr7() {
		return numberofDnaseinChr7;
	}

	public void setNumberofDnaseinChr7(int numberofDnaseinChr7) {
		this.numberofDnaseinChr7 = numberofDnaseinChr7;
	}

	public int getNumberofDnaseinChr8() {
		return numberofDnaseinChr8;
	}

	public void setNumberofDnaseinChr8(int numberofDnaseinChr8) {
		this.numberofDnaseinChr8 = numberofDnaseinChr8;
	}

	public int getNumberofDnaseinChr9() {
		return numberofDnaseinChr9;
	}

	public void setNumberofDnaseinChr9(int numberofDnaseinChr9) {
		this.numberofDnaseinChr9 = numberofDnaseinChr9;
	}

	public int getNumberofDnaseinChr10() {
		return numberofDnaseinChr10;
	}

	public void setNumberofDnaseinChr10(int numberofDnaseinChr10) {
		this.numberofDnaseinChr10 = numberofDnaseinChr10;
	}

	public int getNumberofDnaseinChr11() {
		return numberofDnaseinChr11;
	}

	public void setNumberofDnaseinChr11(int numberofDnaseinChr11) {
		this.numberofDnaseinChr11 = numberofDnaseinChr11;
	}

	public int getNumberofDnaseinChr12() {
		return numberofDnaseinChr12;
	}

	public void setNumberofDnaseinChr12(int numberofDnaseinChr12) {
		this.numberofDnaseinChr12 = numberofDnaseinChr12;
	}

	public int getNumberofDnaseinChr13() {
		return numberofDnaseinChr13;
	}

	public void setNumberofDnaseinChr13(int numberofDnaseinChr13) {
		this.numberofDnaseinChr13 = numberofDnaseinChr13;
	}

	public int getNumberofDnaseinChr14() {
		return numberofDnaseinChr14;
	}

	public void setNumberofDnaseinChr14(int numberofDnaseinChr14) {
		this.numberofDnaseinChr14 = numberofDnaseinChr14;
	}

	public int getNumberofDnaseinChr15() {
		return numberofDnaseinChr15;
	}

	public void setNumberofDnaseinChr15(int numberofDnaseinChr15) {
		this.numberofDnaseinChr15 = numberofDnaseinChr15;
	}

	public int getNumberofDnaseinChr16() {
		return numberofDnaseinChr16;
	}

	public void setNumberofDnaseinChr16(int numberofDnaseinChr16) {
		this.numberofDnaseinChr16 = numberofDnaseinChr16;
	}

	public int getNumberofDnaseinChr17() {
		return numberofDnaseinChr17;
	}

	public void setNumberofDnaseinChr17(int numberofDnaseinChr17) {
		this.numberofDnaseinChr17 = numberofDnaseinChr17;
	}

	public int getNumberofDnaseinChr18() {
		return numberofDnaseinChr18;
	}

	public void setNumberofDnaseinChr18(int numberofDnaseinChr18) {
		this.numberofDnaseinChr18 = numberofDnaseinChr18;
	}

	public int getNumberofDnaseinChr19() {
		return numberofDnaseinChr19;
	}

	public void setNumberofDnaseinChr19(int numberofDnaseinChr19) {
		this.numberofDnaseinChr19 = numberofDnaseinChr19;
	}

	public int getNumberofDnaseinChr20() {
		return numberofDnaseinChr20;
	}

	public void setNumberofDnaseinChr20(int numberofDnaseinChr20) {
		this.numberofDnaseinChr20 = numberofDnaseinChr20;
	}

	public int getNumberofDnaseinChr21() {
		return numberofDnaseinChr21;
	}

	public void setNumberofDnaseinChr21(int numberofDnaseinChr21) {
		this.numberofDnaseinChr21 = numberofDnaseinChr21;
	}

	public int getNumberofDnaseinChr22() {
		return numberofDnaseinChr22;
	}

	public void setNumberofDnaseinChr22(int numberofDnaseinChr22) {
		this.numberofDnaseinChr22 = numberofDnaseinChr22;
	}

	public int getNumberofDnaseinChrX() {
		return numberofDnaseinChrX;
	}

	public void setNumberofDnaseinChrX(int numberofDnaseinChrX) {
		this.numberofDnaseinChrX = numberofDnaseinChrX;
	}

	public int getNumberofDnaseinChrY() {
		return numberofDnaseinChrY;
	}

	public void setNumberofDnaseinChrY(int numberofDnaseinChrY) {
		this.numberofDnaseinChrY = numberofDnaseinChrY;
	}

	public int getNumberofHistoneinChr1() {
		return numberofHistoneinChr1;
	}

	public void setNumberofHistoneinChr1(int numberofHistoneinChr1) {
		this.numberofHistoneinChr1 = numberofHistoneinChr1;
	}

	public int getNumberofHistoneinChr2() {
		return numberofHistoneinChr2;
	}

	public void setNumberofHistoneinChr2(int numberofHistoneinChr2) {
		this.numberofHistoneinChr2 = numberofHistoneinChr2;
	}

	public int getNumberofHistoneinChr3() {
		return numberofHistoneinChr3;
	}

	public void setNumberofHistoneinChr3(int numberofHistoneinChr3) {
		this.numberofHistoneinChr3 = numberofHistoneinChr3;
	}

	public int getNumberofHistoneinChr4() {
		return numberofHistoneinChr4;
	}

	public void setNumberofHistoneinChr4(int numberofHistoneinChr4) {
		this.numberofHistoneinChr4 = numberofHistoneinChr4;
	}

	public int getNumberofHistoneinChr5() {
		return numberofHistoneinChr5;
	}

	public void setNumberofHistoneinChr5(int numberofHistoneinChr5) {
		this.numberofHistoneinChr5 = numberofHistoneinChr5;
	}

	public int getNumberofHistoneinChr6() {
		return numberofHistoneinChr6;
	}

	public void setNumberofHistoneinChr6(int numberofHistoneinChr6) {
		this.numberofHistoneinChr6 = numberofHistoneinChr6;
	}

	public int getNumberofHistoneinChr7() {
		return numberofHistoneinChr7;
	}

	public void setNumberofHistoneinChr7(int numberofHistoneinChr7) {
		this.numberofHistoneinChr7 = numberofHistoneinChr7;
	}

	public int getNumberofHistoneinChr8() {
		return numberofHistoneinChr8;
	}

	public void setNumberofHistoneinChr8(int numberofHistoneinChr8) {
		this.numberofHistoneinChr8 = numberofHistoneinChr8;
	}

	public int getNumberofHistoneinChr9() {
		return numberofHistoneinChr9;
	}

	public void setNumberofHistoneinChr9(int numberofHistoneinChr9) {
		this.numberofHistoneinChr9 = numberofHistoneinChr9;
	}

	public int getNumberofHistoneinChr10() {
		return numberofHistoneinChr10;
	}

	public void setNumberofHistoneinChr10(int numberofHistoneinChr10) {
		this.numberofHistoneinChr10 = numberofHistoneinChr10;
	}

	public int getNumberofHistoneinChr11() {
		return numberofHistoneinChr11;
	}

	public void setNumberofHistoneinChr11(int numberofHistoneinChr11) {
		this.numberofHistoneinChr11 = numberofHistoneinChr11;
	}

	public int getNumberofHistoneinChr12() {
		return numberofHistoneinChr12;
	}

	public void setNumberofHistoneinChr12(int numberofHistoneinChr12) {
		this.numberofHistoneinChr12 = numberofHistoneinChr12;
	}

	public int getNumberofHistoneinChr13() {
		return numberofHistoneinChr13;
	}

	public void setNumberofHistoneinChr13(int numberofHistoneinChr13) {
		this.numberofHistoneinChr13 = numberofHistoneinChr13;
	}

	public int getNumberofHistoneinChr14() {
		return numberofHistoneinChr14;
	}

	public void setNumberofHistoneinChr14(int numberofHistoneinChr14) {
		this.numberofHistoneinChr14 = numberofHistoneinChr14;
	}

	public int getNumberofHistoneinChr15() {
		return numberofHistoneinChr15;
	}

	public void setNumberofHistoneinChr15(int numberofHistoneinChr15) {
		this.numberofHistoneinChr15 = numberofHistoneinChr15;
	}

	public int getNumberofHistoneinChr16() {
		return numberofHistoneinChr16;
	}

	public void setNumberofHistoneinChr16(int numberofHistoneinChr16) {
		this.numberofHistoneinChr16 = numberofHistoneinChr16;
	}

	public int getNumberofHistoneinChr17() {
		return numberofHistoneinChr17;
	}

	public void setNumberofHistoneinChr17(int numberofHistoneinChr17) {
		this.numberofHistoneinChr17 = numberofHistoneinChr17;
	}

	public int getNumberofHistoneinChr18() {
		return numberofHistoneinChr18;
	}

	public void setNumberofHistoneinChr18(int numberofHistoneinChr18) {
		this.numberofHistoneinChr18 = numberofHistoneinChr18;
	}

	public int getNumberofHistoneinChr19() {
		return numberofHistoneinChr19;
	}

	public void setNumberofHistoneinChr19(int numberofHistoneinChr19) {
		this.numberofHistoneinChr19 = numberofHistoneinChr19;
	}

	public int getNumberofHistoneinChr20() {
		return numberofHistoneinChr20;
	}

	public void setNumberofHistoneinChr20(int numberofHistoneinChr20) {
		this.numberofHistoneinChr20 = numberofHistoneinChr20;
	}

	public int getNumberofHistoneinChr21() {
		return numberofHistoneinChr21;
	}

	public void setNumberofHistoneinChr21(int numberofHistoneinChr21) {
		this.numberofHistoneinChr21 = numberofHistoneinChr21;
	}

	public int getNumberofHistoneinChr22() {
		return numberofHistoneinChr22;
	}

	public void setNumberofHistoneinChr22(int numberofHistoneinChr22) {
		this.numberofHistoneinChr22 = numberofHistoneinChr22;
	}

	public int getNumberofHistoneinChrX() {
		return numberofHistoneinChrX;
	}

	public void setNumberofHistoneinChrX(int numberofHistoneinChrX) {
		this.numberofHistoneinChrX = numberofHistoneinChrX;
	}

	public int getNumberofHistoneinChrY() {
		return numberofHistoneinChrY;
	}

	public void setNumberofHistoneinChrY(int numberofHistoneinChrY) {
		this.numberofHistoneinChrY = numberofHistoneinChrY;
	}

	public int getNumberofTfbsinChr1() {
		return numberofTfbsinChr1;
	}

	public void setNumberofTfbsinChr1(int numberofTfbsinChr1) {
		this.numberofTfbsinChr1 = numberofTfbsinChr1;
	}

	public int getNumberofTfbsinChr2() {
		return numberofTfbsinChr2;
	}

	public void setNumberofTfbsinChr2(int numberofTfbsinChr2) {
		this.numberofTfbsinChr2 = numberofTfbsinChr2;
	}

	public int getNumberofTfbsinChr3() {
		return numberofTfbsinChr3;
	}

	public void setNumberofTfbsinChr3(int numberofTfbsinChr3) {
		this.numberofTfbsinChr3 = numberofTfbsinChr3;
	}

	public int getNumberofTfbsinChr4() {
		return numberofTfbsinChr4;
	}

	public void setNumberofTfbsinChr4(int numberofTfbsinChr4) {
		this.numberofTfbsinChr4 = numberofTfbsinChr4;
	}

	public int getNumberofTfbsinChr5() {
		return numberofTfbsinChr5;
	}

	public void setNumberofTfbsinChr5(int numberofTfbsinChr5) {
		this.numberofTfbsinChr5 = numberofTfbsinChr5;
	}

	public int getNumberofTfbsinChr6() {
		return numberofTfbsinChr6;
	}

	public void setNumberofTfbsinChr6(int numberofTfbsinChr6) {
		this.numberofTfbsinChr6 = numberofTfbsinChr6;
	}

	public int getNumberofTfbsinChr7() {
		return numberofTfbsinChr7;
	}

	public void setNumberofTfbsinChr7(int numberofTfbsinChr7) {
		this.numberofTfbsinChr7 = numberofTfbsinChr7;
	}

	public int getNumberofTfbsinChr8() {
		return numberofTfbsinChr8;
	}

	public void setNumberofTfbsinChr8(int numberofTfbsinChr8) {
		this.numberofTfbsinChr8 = numberofTfbsinChr8;
	}

	public int getNumberofTfbsinChr9() {
		return numberofTfbsinChr9;
	}

	public void setNumberofTfbsinChr9(int numberofTfbsinChr9) {
		this.numberofTfbsinChr9 = numberofTfbsinChr9;
	}

	public int getNumberofTfbsinChr10() {
		return numberofTfbsinChr10;
	}

	public void setNumberofTfbsinChr10(int numberofTfbsinChr10) {
		this.numberofTfbsinChr10 = numberofTfbsinChr10;
	}

	public int getNumberofTfbsinChr11() {
		return numberofTfbsinChr11;
	}

	public void setNumberofTfbsinChr11(int numberofTfbsinChr11) {
		this.numberofTfbsinChr11 = numberofTfbsinChr11;
	}

	public int getNumberofTfbsinChr12() {
		return numberofTfbsinChr12;
	}

	public void setNumberofTfbsinChr12(int numberofTfbsinChr12) {
		this.numberofTfbsinChr12 = numberofTfbsinChr12;
	}

	public int getNumberofTfbsinChr13() {
		return numberofTfbsinChr13;
	}

	public void setNumberofTfbsinChr13(int numberofTfbsinChr13) {
		this.numberofTfbsinChr13 = numberofTfbsinChr13;
	}

	public int getNumberofTfbsinChr14() {
		return numberofTfbsinChr14;
	}

	public void setNumberofTfbsinChr14(int numberofTfbsinChr14) {
		this.numberofTfbsinChr14 = numberofTfbsinChr14;
	}

	public int getNumberofTfbsinChr15() {
		return numberofTfbsinChr15;
	}

	public void setNumberofTfbsinChr15(int numberofTfbsinChr15) {
		this.numberofTfbsinChr15 = numberofTfbsinChr15;
	}

	public int getNumberofTfbsinChr16() {
		return numberofTfbsinChr16;
	}

	public void setNumberofTfbsinChr16(int numberofTfbsinChr16) {
		this.numberofTfbsinChr16 = numberofTfbsinChr16;
	}

	public int getNumberofTfbsinChr17() {
		return numberofTfbsinChr17;
	}

	public void setNumberofTfbsinChr17(int numberofTfbsinChr17) {
		this.numberofTfbsinChr17 = numberofTfbsinChr17;
	}

	public int getNumberofTfbsinChr18() {
		return numberofTfbsinChr18;
	}

	public void setNumberofTfbsinChr18(int numberofTfbsinChr18) {
		this.numberofTfbsinChr18 = numberofTfbsinChr18;
	}

	public int getNumberofTfbsinChr19() {
		return numberofTfbsinChr19;
	}

	public void setNumberofTfbsinChr19(int numberofTfbsinChr19) {
		this.numberofTfbsinChr19 = numberofTfbsinChr19;
	}

	public int getNumberofTfbsinChr20() {
		return numberofTfbsinChr20;
	}

	public void setNumberofTfbsinChr20(int numberofTfbsinChr20) {
		this.numberofTfbsinChr20 = numberofTfbsinChr20;
	}

	public int getNumberofTfbsinChr21() {
		return numberofTfbsinChr21;
	}

	public void setNumberofTfbsinChr21(int numberofTfbsinChr21) {
		this.numberofTfbsinChr21 = numberofTfbsinChr21;
	}

	public int getNumberofTfbsinChr22() {
		return numberofTfbsinChr22;
	}

	public void setNumberofTfbsinChr22(int numberofTfbsinChr22) {
		this.numberofTfbsinChr22 = numberofTfbsinChr22;
	}

	public int getNumberofTfbsinChrX() {
		return numberofTfbsinChrX;
	}

	public void setNumberofTfbsinChrX(int numberofTfbsinChrX) {
		this.numberofTfbsinChrX = numberofTfbsinChrX;
	}

	public int getNumberofTfbsinChrY() {
		return numberofTfbsinChrY;
	}

	public void setNumberofTfbsinChrY(int numberofTfbsinChrY) {
		this.numberofTfbsinChrY = numberofTfbsinChrY;
	}

	public FileWriter getChr1FileWriter() {
		return chr1FileWriter;
	}

	public void setChr1FileWriter(FileWriter chr1FileWriter) {
		this.chr1FileWriter = chr1FileWriter;
	}

	public FileWriter getChr2FileWriter() {
		return chr2FileWriter;
	}

	public void setChr2FileWriter(FileWriter chr2FileWriter) {
		this.chr2FileWriter = chr2FileWriter;
	}

	public FileWriter getChr3FileWriter() {
		return chr3FileWriter;
	}

	public void setChr3FileWriter(FileWriter chr3FileWriter) {
		this.chr3FileWriter = chr3FileWriter;
	}

	public FileWriter getChr4FileWriter() {
		return chr4FileWriter;
	}

	public void setChr4FileWriter(FileWriter chr4FileWriter) {
		this.chr4FileWriter = chr4FileWriter;
	}

	public FileWriter getChr5FileWriter() {
		return chr5FileWriter;
	}

	public void setChr5FileWriter(FileWriter chr5FileWriter) {
		this.chr5FileWriter = chr5FileWriter;
	}

	public FileWriter getChr6FileWriter() {
		return chr6FileWriter;
	}

	public void setChr6FileWriter(FileWriter chr6FileWriter) {
		this.chr6FileWriter = chr6FileWriter;
	}

	public FileWriter getChr7FileWriter() {
		return chr7FileWriter;
	}

	public void setChr7FileWriter(FileWriter chr7FileWriter) {
		this.chr7FileWriter = chr7FileWriter;
	}

	public FileWriter getChr8FileWriter() {
		return chr8FileWriter;
	}

	public void setChr8FileWriter(FileWriter chr8FileWriter) {
		this.chr8FileWriter = chr8FileWriter;
	}

	public FileWriter getChr9FileWriter() {
		return chr9FileWriter;
	}

	public void setChr9FileWriter(FileWriter chr9FileWriter) {
		this.chr9FileWriter = chr9FileWriter;
	}

	public FileWriter getChr10FileWriter() {
		return chr10FileWriter;
	}

	public void setChr10FileWriter(FileWriter chr10FileWriter) {
		this.chr10FileWriter = chr10FileWriter;
	}

	public FileWriter getChr11FileWriter() {
		return chr11FileWriter;
	}

	public void setChr11FileWriter(FileWriter chr11FileWriter) {
		this.chr11FileWriter = chr11FileWriter;
	}

	public FileWriter getChr12FileWriter() {
		return chr12FileWriter;
	}

	public void setChr12FileWriter(FileWriter chr12FileWriter) {
		this.chr12FileWriter = chr12FileWriter;
	}

	public FileWriter getChr13FileWriter() {
		return chr13FileWriter;
	}

	public void setChr13FileWriter(FileWriter chr13FileWriter) {
		this.chr13FileWriter = chr13FileWriter;
	}

	public FileWriter getChr14FileWriter() {
		return chr14FileWriter;
	}

	public void setChr14FileWriter(FileWriter chr14FileWriter) {
		this.chr14FileWriter = chr14FileWriter;
	}

	public FileWriter getChr15FileWriter() {
		return chr15FileWriter;
	}

	public void setChr15FileWriter(FileWriter chr15FileWriter) {
		this.chr15FileWriter = chr15FileWriter;
	}

	public FileWriter getChr16FileWriter() {
		return chr16FileWriter;
	}

	public void setChr16FileWriter(FileWriter chr16FileWriter) {
		this.chr16FileWriter = chr16FileWriter;
	}

	public FileWriter getChr17FileWriter() {
		return chr17FileWriter;
	}

	public void setChr17FileWriter(FileWriter chr17FileWriter) {
		this.chr17FileWriter = chr17FileWriter;
	}

	public FileWriter getChr18FileWriter() {
		return chr18FileWriter;
	}

	public void setChr18FileWriter(FileWriter chr18FileWriter) {
		this.chr18FileWriter = chr18FileWriter;
	}

	public FileWriter getChr19FileWriter() {
		return chr19FileWriter;
	}

	public void setChr19FileWriter(FileWriter chr19FileWriter) {
		this.chr19FileWriter = chr19FileWriter;
	}

	public FileWriter getChr20FileWriter() {
		return chr20FileWriter;
	}

	public void setChr20FileWriter(FileWriter chr20FileWriter) {
		this.chr20FileWriter = chr20FileWriter;
	}

	public FileWriter getChr21FileWriter() {
		return chr21FileWriter;
	}

	public void setChr21FileWriter(FileWriter chr21FileWriter) {
		this.chr21FileWriter = chr21FileWriter;
	}

	public FileWriter getChr22FileWriter() {
		return chr22FileWriter;
	}

	public void setChr22FileWriter(FileWriter chr22FileWriter) {
		this.chr22FileWriter = chr22FileWriter;
	}

	public FileWriter getChrXFileWriter() {
		return chrXFileWriter;
	}

	public void setChrXFileWriter(FileWriter chrXFileWriter) {
		this.chrXFileWriter = chrXFileWriter;
	}

	public FileWriter getChrYFileWriter() {
		return chrYFileWriter;
	}

	public void setChrYFileWriter(FileWriter chrYFileWriter) {
		this.chrYFileWriter = chrYFileWriter;
	}

	public BufferedWriter getChr1BufferedWriter() {
		return chr1BufferedWriter;
	}

	public void setChr1BufferedWriter(BufferedWriter chr1BufferedWriter) {
		this.chr1BufferedWriter = chr1BufferedWriter;
	}

	public BufferedWriter getChr2BufferedWriter() {
		return chr2BufferedWriter;
	}

	public void setChr2BufferedWriter(BufferedWriter chr2BufferedWriter) {
		this.chr2BufferedWriter = chr2BufferedWriter;
	}

	public BufferedWriter getChr3BufferedWriter() {
		return chr3BufferedWriter;
	}

	public void setChr3BufferedWriter(BufferedWriter chr3BufferedWriter) {
		this.chr3BufferedWriter = chr3BufferedWriter;
	}

	public BufferedWriter getChr4BufferedWriter() {
		return chr4BufferedWriter;
	}

	public void setChr4BufferedWriter(BufferedWriter chr4BufferedWriter) {
		this.chr4BufferedWriter = chr4BufferedWriter;
	}

	public BufferedWriter getChr5BufferedWriter() {
		return chr5BufferedWriter;
	}

	public void setChr5BufferedWriter(BufferedWriter chr5BufferedWriter) {
		this.chr5BufferedWriter = chr5BufferedWriter;
	}

	public BufferedWriter getChr6BufferedWriter() {
		return chr6BufferedWriter;
	}

	public void setChr6BufferedWriter(BufferedWriter chr6BufferedWriter) {
		this.chr6BufferedWriter = chr6BufferedWriter;
	}

	public BufferedWriter getChr7BufferedWriter() {
		return chr7BufferedWriter;
	}

	public void setChr7BufferedWriter(BufferedWriter chr7BufferedWriter) {
		this.chr7BufferedWriter = chr7BufferedWriter;
	}

	public BufferedWriter getChr8BufferedWriter() {
		return chr8BufferedWriter;
	}

	public void setChr8BufferedWriter(BufferedWriter chr8BufferedWriter) {
		this.chr8BufferedWriter = chr8BufferedWriter;
	}

	public BufferedWriter getChr9BufferedWriter() {
		return chr9BufferedWriter;
	}

	public void setChr9BufferedWriter(BufferedWriter chr9BufferedWriter) {
		this.chr9BufferedWriter = chr9BufferedWriter;
	}

	public BufferedWriter getChr10BufferedWriter() {
		return chr10BufferedWriter;
	}

	public void setChr10BufferedWriter(BufferedWriter chr10BufferedWriter) {
		this.chr10BufferedWriter = chr10BufferedWriter;
	}

	public BufferedWriter getChr11BufferedWriter() {
		return chr11BufferedWriter;
	}

	public void setChr11BufferedWriter(BufferedWriter chr11BufferedWriter) {
		this.chr11BufferedWriter = chr11BufferedWriter;
	}

	public BufferedWriter getChr12BufferedWriter() {
		return chr12BufferedWriter;
	}

	public void setChr12BufferedWriter(BufferedWriter chr12BufferedWriter) {
		this.chr12BufferedWriter = chr12BufferedWriter;
	}

	public BufferedWriter getChr13BufferedWriter() {
		return chr13BufferedWriter;
	}

	public void setChr13BufferedWriter(BufferedWriter chr13BufferedWriter) {
		this.chr13BufferedWriter = chr13BufferedWriter;
	}

	public BufferedWriter getChr14BufferedWriter() {
		return chr14BufferedWriter;
	}

	public void setChr14BufferedWriter(BufferedWriter chr14BufferedWriter) {
		this.chr14BufferedWriter = chr14BufferedWriter;
	}

	public BufferedWriter getChr15BufferedWriter() {
		return chr15BufferedWriter;
	}

	public void setChr15BufferedWriter(BufferedWriter chr15BufferedWriter) {
		this.chr15BufferedWriter = chr15BufferedWriter;
	}

	public BufferedWriter getChr16BufferedWriter() {
		return chr16BufferedWriter;
	}

	public void setChr16BufferedWriter(BufferedWriter chr16BufferedWriter) {
		this.chr16BufferedWriter = chr16BufferedWriter;
	}

	public BufferedWriter getChr17BufferedWriter() {
		return chr17BufferedWriter;
	}

	public void setChr17BufferedWriter(BufferedWriter chr17BufferedWriter) {
		this.chr17BufferedWriter = chr17BufferedWriter;
	}

	public BufferedWriter getChr18BufferedWriter() {
		return chr18BufferedWriter;
	}

	public void setChr18BufferedWriter(BufferedWriter chr18BufferedWriter) {
		this.chr18BufferedWriter = chr18BufferedWriter;
	}

	public BufferedWriter getChr19BufferedWriter() {
		return chr19BufferedWriter;
	}

	public void setChr19BufferedWriter(BufferedWriter chr19BufferedWriter) {
		this.chr19BufferedWriter = chr19BufferedWriter;
	}

	public BufferedWriter getChr20BufferedWriter() {
		return chr20BufferedWriter;
	}

	public void setChr20BufferedWriter(BufferedWriter chr20BufferedWriter) {
		this.chr20BufferedWriter = chr20BufferedWriter;
	}

	public BufferedWriter getChr21BufferedWriter() {
		return chr21BufferedWriter;
	}

	public void setChr21BufferedWriter(BufferedWriter chr21BufferedWriter) {
		this.chr21BufferedWriter = chr21BufferedWriter;
	}

	public BufferedWriter getChr22BufferedWriter() {
		return chr22BufferedWriter;
	}

	public void setChr22BufferedWriter(BufferedWriter chr22BufferedWriter) {
		this.chr22BufferedWriter = chr22BufferedWriter;
	}

	public BufferedWriter getChrXBufferedWriter() {
		return chrXBufferedWriter;
	}

	public void setChrXBufferedWriter(BufferedWriter chrXBufferedWriter) {
		this.chrXBufferedWriter = chrXBufferedWriter;
	}

	public BufferedWriter getChrYBufferedWriter() {
		return chrYBufferedWriter;
	}

	public void setChrYBufferedWriter(BufferedWriter chrYBufferedWriter) {
		this.chrYBufferedWriter = chrYBufferedWriter;
	}





	int totalNumberofTfbs;
	int totalNumberofHistone;
	int totalNumberofDnase;
	
	public int getTotalNumberofTfbs(){
		return numberofTfbsinChr1 + numberofTfbsinChr2 + numberofTfbsinChr3 + numberofTfbsinChr4 + numberofTfbsinChr5 + numberofTfbsinChr6 + numberofTfbsinChr7 + numberofTfbsinChr8 + numberofTfbsinChr9 + numberofTfbsinChr10 + numberofTfbsinChr11 + numberofTfbsinChr12 + numberofTfbsinChr13 + numberofTfbsinChr14 + numberofTfbsinChr15 + numberofTfbsinChr16 + numberofTfbsinChr17 + numberofTfbsinChr18 + numberofTfbsinChr19 + numberofTfbsinChr20 + numberofTfbsinChr21 + numberofTfbsinChr22 + numberofTfbsinChrX + numberofTfbsinChrY;  
	}
	
	public int getTotalNumberofHistone(){
		return numberofHistoneinChr1 + numberofHistoneinChr2 + numberofHistoneinChr3 + numberofHistoneinChr4 + numberofHistoneinChr5 + numberofHistoneinChr6 + numberofHistoneinChr7 + numberofHistoneinChr8 + numberofHistoneinChr9 + numberofHistoneinChr10 + numberofHistoneinChr11 + numberofHistoneinChr12 + numberofHistoneinChr13 + numberofHistoneinChr14 + numberofHistoneinChr15 + numberofHistoneinChr16 + numberofHistoneinChr17 + numberofHistoneinChr18 + numberofHistoneinChr19 + numberofHistoneinChr20 + numberofHistoneinChr21 + numberofHistoneinChr22 + numberofHistoneinChrX + numberofHistoneinChrY;  
	}
	
	public int getTotalNumberofDnase(){
		return numberofDnaseinChr1 + numberofDnaseinChr2 + numberofDnaseinChr3 + numberofDnaseinChr4 + numberofDnaseinChr5 + numberofDnaseinChr6 + numberofDnaseinChr7 + numberofDnaseinChr8 + numberofDnaseinChr9 + numberofDnaseinChr10 + numberofDnaseinChr11 + numberofDnaseinChr12 + numberofDnaseinChr13 + numberofDnaseinChr14 + numberofDnaseinChr15 + numberofDnaseinChr16 + numberofDnaseinChr17 + numberofDnaseinChr18 + numberofDnaseinChr19 + numberofDnaseinChr20 + numberofDnaseinChr21 + numberofDnaseinChr22 + numberofDnaseinChrX + numberofDnaseinChrY;  
	}
			
	
	
	
}
